Membrane-bound ARF1 peptide: interpretation of neutron diffraction data by molecular dynamics simulation methods.

Adenosine diphosphate ribosylation factor-1 (ARF1) is activated by cell membrane binding of a self-folding N-terminal domain. We have previously presented four possible conformations of the membrane bound, human ARF1 N-terminal peptide in planar lipid bilayers of DOPC and DOPG (7:3 molar ratio), determined from lamellar neutron diffraction and circular dichroism data. In this paper we analyse the four possible conformations by molecular dynamics simulations. The aim of these simulations was to use MD to distinguish which of the four possible membrane bound structures was the most likely. The most likely conformation was determined according to the following criteria: (a) location of label positions on the peptide in relation to the bilayer, (b) lowest mean square displacement from the initial structure, (c) lowest system energy, (d) most peptide-lipid headgroup hydrogen bonding, (e) analysis of phi/psi angles of the peptide. These findings demonstrate the application of molecular dynamics simulations to explore neutron diffraction data.

Molecular dynamics simulations of a mixed DOPC/DOPG bilayer.

We have constructed a mixed dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol bilayer (DOPG) bilayer utilizing MD simulations. The aim was to develop an explicit molecular model of biological membranes as a complementary technique to neutron diffraction studies that are well established within the group. A monolayer was constructed by taking a previously customized PDB file of each molecule and arranging them in a seven rows of ten molecules and duplicated and rotated to form a bilayer. The 140-molecule bilayer contained 98 DOPC molecules and 42 DOPG molecules, in a 7:3 ratio in favour of DOPC. Sodium counter ions were placed near the phosphate moiety of DOPG to counteract the negative charge of DOPG. This was representative of the lipid ratio in a sample used for neutron diffraction. The MD package GROMACS was used for confining the bilayer in a triclinic box, adding Simple Polar Charge water molecules, energy minimization (EM). The bilayer/solvent system was subjected to EM using the steepest descent method to nullify bad contacts and reduce the potential energy of the system. Subsequent MD simulation using an initial NVT (constant number of particles, volume and temperature) for a 20 ps MD run followed by a NPT (constant number of particles, pressure and temperature) was performed. Structural parameters including volume of lipid, area of lipid, order parameter of the fatty acyl carbons and electron density profiles generated by the MD simulation were verified with values obtained from experimental data of DOPC, as there are no comparable experimental data available for the mixed bilayer.

Inhibitors can arrest the membrane activity of human islet amyloid polypeptide independently of amyloid formation.

Human islet amyloid polypeptide (hIAPP), co-secreted with insulin from pancreatic beta cells, misfolds to form amyloid deposits in non-insulin-dependent diabetes mellitus (NIDDM). Like many amyloidogenic proteins, hIAPP is membrane-active: this may be significant in the pathogenesis of NIDDM. Non-fibrillar hIAPP induces electrical and physical breakdown in planar lipid bilayers, and IAPP inserts spontaneously into lipid monolayers, markedly increasing their surface area and producing Brewster angle microscopy reflectance changes. Congo red inhibits these activities, and they are completely arrested by rifampicin, despite continued amyloid formation. Our results support the idea that non-fibrillar IAPP is membrane-active, and may have implications for therapy and for structural studies of membrane-active amyloid.

Oblique membrane insertion of viral fusion peptide probed by neutron diffraction.

Fusion peptides mimic the membrane fusion activities of the larger viral proteins from which they derive their sequences. A possible mode of activity involves their oblique insertion into lipid bilayers, causing membrane disruption by promoting highly curved hemifusion intermediates, leading to fusion. We have determined the location and orientation of the simian immunodeficiency virus (SIV) fusion peptide in planar lipid bilayers using neutron lamellar diffraction. The helical axis of the peptide adopts an angle of 55 degrees relative to the membrane normal, while it positions itself nearest the lipid bilayer surface. This is the first direct observation of the structural interaction between a fusion peptide and a phospholipid bilayer.

Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data.

Neutron-diffraction data were collected from stacked bilayers of 1, 2-dioleoyl-sn-glycero-phosphocholine under conditions of increasing relative humidity at both 0 and 8.06% (2)H(2)O. Over the period of data collection, the d-repeat of both swelling-series samples increased. Each family of structure factors, representing each of the five orders of diffraction, are shown to lie on smooth curves, allowing structure factors of intermediate d-repeat to be determined. In the case of the 8.06% (2)H(2)O data, but not the 0% (2)H(2)O data, all observed structure factors lie on a single continuous transform. 8.06% (2)H(2)O has a net neutron-scattering density of zero; its use in neutron-diffraction experiments presents a novel application of the so-called 'minus fluid' approach, without mathematical manipulation. The data are used to demonstrate the increased accuracy inherent in this real-time swelling-series approach. A quantitative analysis of errors caused by differences in d--repeat in difference subtractions is presented.

X-ray diffraction study of feline leukemia virus fusion peptide and lipid polymorphism.

The structural effects of the fusion peptide of feline leukemia virus (FeLV) on the lipid polymorphism of N-methylated dioleoylphosphatidylethanolamine were studied using a temperature ramp with sequential X-ray diffraction. This peptide, the hydrophobic amino-terminus of p15E, has been proven to be fusogenic and to promote the formation of highly curved, intermediate structures on the lamellar liquid-crystal to inverse hexagonal phase transition pathway. The FeLV peptide produces marked effects on the thermotropic mesomorphic behaviour of MeDOPE, a phospholipid with an intermediate spontaneous radius of curvature. The peptide is shown to reduce the lamellar repeat distance of the membrane prior to the onset of an inverted cubic phase. This suggests that membrane thinning may play a role in peptide-induced membrane fusion and strengthens the link between the fusion pathway and inverted cubic phase formation. The results of this study are interpreted in relation to models of the membrane fusion mechanism.

Orientation of the headgroup of phosphatidylinositol in a model biomembrane as determined by neutron diffraction.

Derivatives of the sodium salt of dimyristoylphosphatidylinositol (DMPI) have been synthesized specifically deuterated in the headgroup. A 50:50 (molar) mixture of DMPI with dimyristoylphosphatidylcholine (DMPC) hydrated to the level of 16 waters/lipid gives a biomembrane-like Lalpha phase at 50 degrees C. Comparison of the neutron diffraction scattering profiles for deuterated and undeuterated membranes allowed the depth of each deuterium (hydrogen) within the bilayer to be determined to +/-0.5 A. This gave the orientation of the inositol ring which lies more-or-less along the bilayer normal projecting directly out into the water. This orientation is similar to that of the sugar residue in glycolipids and confirms previous models for PI. On the assumption that the (P)O-DAG bond is more-or-less parallel to the bilayer normal, it is consistent with a roughly trans, trans, trans, gauche- conformation for the glyceryl-phosphate-inositol link. In the case of DMPI, it is the C4-hydroxy group which is most fully extended into the water layer, but when this is phosphorylated, the inositol ring turns over and tilts so that the C5-hydroxy group is now the one furthest extended into the water layer. Hence, at each stage in the pathway PI --> PI-4P --> PI-4,5-P2, it is the hydroxy position most exposed to the water which undergoes phosphorylation. Whereas the orientation of the inositol ring in DMPI can be seen simply as maximizing its hydration, the tilt of the ring in DMPI-4P cannot be explained in this way. It is suggested that it is due to an electrostatic interaction.

Interaction of substance P with phospholipid bilayers: A neutron diffraction study.

Neutron diffraction has been used to study the membrane-bound structure of substance P (SP), a member of the tachykinin family of neuropeptides. The depth of penetration of its C-terminus in zwitterionic and anionic phospholipid bilayers was probed by specific deuteration of leucine 10, the penultimate amino acid residue. The results show that the interaction of SP with bilayers, composed of either dioleoylphosphatidylcholine (DOPC), or a 50:50 mixture of DOPC and the anionic phospholipid dioleoylphosphatidylglycerol (DOPG), takes place at two locations. One requires insertion of the peptide into the hydrophobic region of the bilayer, the other is much more peripheral. The penetration of the peptide into the hydrophobic region of the bilayer is reflected in a marked difference in the water distribution profiles. SP is seen to insert into DOPC bilayers, but a larger proportion of the peptide is found at the surface when compared to the anionic bilayers. The positions of the two label populations show only minor differences between the two types of bilayer.

Modulation of lipid polymorphism by the feline leukemia virus fusion peptide: implications for the fusion mechanism.

The structural effects of the fusion peptide of feline leukemia virus (FeLV) on lipid polymorphism were studied, using differential scanning calorimetry (DSC), 31P nuclear magnetic resonance (NMR), and time-resolved X-ray diffraction. This peptide lowers the bilayer to inverted hexagonal phase transition temperature, TH, of dipalmitoleoylphosphatidylethanolamine (DiPoPE) at peptide mole fractions of up to 1.5 x 10(-3) at pH 5.0 and at pH 7.4. The temperature at which isotropic 31P NMR signals for monomethyldioleoylphosphatidylethanolamine (MeDOPE) first occurred is lowered by the FeLV peptide. The amount of isotropic signal seen at 40 degrees C is directly correlated to the peptide:lipid molar ratio. In the peptide-containing samples, more lipid remains in the isotropic state over the whole recorded temperature range. Isotropic 31P NMR signals were observed for DiPoPE in the presence of the FeLV peptide for the entire recorded temperature range of 35-50 degrees C, while pure DiPoPE showed no significant amount of isotropic signal. X-ray studies of DiPoPE show the formation of a new lipid phase with peptide, which is not seen in the pure lipid samples. Disordering of the Lalpha phase is evidenced by broadening of the diffraction peaks, and the hexagonal cell parameter is decreased with peptide present. Our results suggest that the FeLV peptide is increasing the negative curvature of the lipid system, which is thought to be crucial to the formation of highly bent, high-energy structural fusion intermediates, such as the "stalk" model. Fusion activity for this putative fusogenic peptide was also demonstrated, using a resonance energy transfer (RET) lipid mixing assay. To our knowledge, this work provides the first published experimental evidence of both fusogenic activity and effects on lipid polymorphism for the FeLV fusion peptide.

Structural plasticity of the feline leukaemia virus fusion peptide: a circular dichroism study.

The secondary structure of the feline leukaemia virus (FeLV) fusion peptide was investigated using circular dichroism (CD). Our results show that this peptide can readily flip between random, alpha-helical and beta-sheet conformations, depending upon its environment. The CD spectrum changes from one characteristic of random coil to predominantly beta-sheet type, and finally to that showing the characteristics of alpha-helical structure on moving from an aqueous solvent, through several increasingly hydrophobic systems, to a highly hydrophobic solvent. Electron microscopy confirmed the presence of beta structure. We propose that the structural plasticity demonstrated here is crucial to the ability of the fusion peptide to perturb lipid bilayers, and thus promote membrane fusion.

The headgroup orientation of dimyristoylphosphatidylinositol-4-phosphate in mixed lipid bilayers: a neutron diffraction study.

The trisodium salt of dimyristoylphosphatidylinositol-4-phosphate (DMPI-4P) has been synthesised specifically deuterated at particular sites in the headgroup. These materials have been used in neutron diffraction experiments, which successfully located the position (depth) of each of these deuterated sites to within +/- 0.5 A in a mixed model membrane (a 1:1 molar mixture of DMPI-4P with dimyristoyl-phosphatidylcholine, DMPC, in the L alpha phase, hydrated to the level of 28 water molecules per lipid molecule). The diffracted intensities were measured at four different D2O/H2O ratios and six orders of diffraction were obtained. These data sets, in conjunction with computer modelling, have been used to determine the orientation of the inositol ring of DMPI-4P, localising each vertical H-H distance to within approximately +/- 0.03 A. The orientation of the inositol ring is found to be one in which the C5 hydroxyl is extended out into the aqueous medium. This is, therefore, the most accessible site for water-borne reagents. This may be significant for the important pathway leading from PI-4P to PI-4,5P2. On the assumption that the P/ODAG bond is orientated parallel to the bilayer normal, these results are consistent with two possible conformations for the portion of the headgroup connecting the diacylglycerol to the inositol ring. Distinction between these two is difficult, but one may be favoured since the other involves close atom-atom contacts.

Phosphatydylglycerol promotes bilayer insertion of salmon calcitonin.

Neutron diffraction from oriented multibilayers has been used to study the bilayer interaction of the amphipathic peptide salmon calcitonin. Penetration of calcitonin into bilayers composed of dioleoylphosphatidylcholine increases with the addition of 15% (mol) of the anionic phospholipid dioleoylphosphatidylglycerol. Neutron scattering profiles of water distribution in stacked bilayers show a continuous band of deuterons across each bilayer, consistent with the suggestion that the hormone forms transbilayer alpha-helixes under these conditions. These experiments add to the growing body of data on the role of phosphatidylglycerol in bilayer insertion of protein helices and suggests a possible evolutionary history for calcitonin.

Neutron diffraction reveals the orientation of the headgroup of inositol lipids in model membranes.

Neutron diffraction studies show that the inositol ring in the headgroup of phosphatidylinositol extends perpendicular to the membrane surface but that phosphorylation of the 4-position causes the ring to tilt over.

Neutron diffraction studies of amphipathic helices in phospholipid bilayers.

The structural feature which is thought to facilitate the interaction of many peptides with phospholipid bilayers is the ability to fold into an amphipathic helix. In most cases the exact location and orientation of this helix with respect to the membrane is not known, and may vary with factors such as pH and phospholipid content of the bilayer. The growing interest in this area is stimulated by indications that similar interactions can contribute to the binding of certain hormones to their cell-surface receptors. We have been using the techniques of neutron diffraction from stacked phospholipid bilayers in an attempt to investigate this phenomenon with a number of membrane-active peptides. Here we report some of our findings with three of these: the bee venom melittin; the hormone calcitonin; and a synthetic peptide representing the ion channel fragment of influenza A M2 protein.

Changes in intracellular calcium concentration in bovine oocytes following penetration by spermatozoa.

The pattern of changes in intracellular calcium concentration ([Ca2+]i) in bovine oocytes after penetration by spermatozoa was determined. Dynamic video imaging, using Fura-2 as a probe for intracellular free calcium, showed that activation of oocytes by spermatozoa induced multiple transient increases in [Ca2+]i with a spike interval of 24.2 +/- 7.3 min, and that the early transient increases were propagated throughout the oocytes in the form of a wave. Calcium transients at fertilization are involved in the induction of cortical granule exocytosis and the resultant block to polyspermy. The hypothesis that the inhibition of Ca2+ release from inositol trisphosphate-sensitive stores would inhibit exocytosis and increase polyspermy was tested by injecting oocytes before fertilization with heparin, a potent inhibitor of inositol trisphosphate-activated Ca2+ release. There was no significant difference after fertilization in either [Ca2+]i spikes or in polyspermy rates between control and experimental groups injected with low molecular mass heparin up to a final cytoplasmic concentration of 400 mumol l-1. We conclude that inositol trisphosphate-independent Ca2+ stores may be mobilized during the fertilization of bovine oocytes.

Neutron diffraction reveals the site of amantadine blockade in the influenza A M2 ion channel.

The influenza A M2 protein forms proton channels which are blocked by the anti-influenza drug amantadine. Using the technique of neutron diffraction with both deuterium-labeled amantadine and influenza A M2 peptides, this study has directly located the position of interaction between the drug and the transmembrane domain of M2. Amantadine is found 0.5 nm from the center of the bilayer in an area between Val 27 and Ser 31, a location consistent with the formation of a steric block within the ion channel. Similar experiments with amantadine and an amantadine-resistant mutant peptide showed no such interaction.

A combined X-ray and neutron diffraction study of selectively deuterated melittin in phospholipid bilayers: effect of pH.

In order to study consequences of protonation of the N-terminus upon the interaction of the bee venom melittin with phospholipid bilayers, analogues of melittin, some of which were specifically deuterated at either Ala-12 or 15, were synthesized. These peptides were incorporated into bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine at either low pH (N-terminus protonated) or high pH (N-terminus unprotonated). X-ray and neutron diffraction data were collected from ordered stacks of these bilayers and from peptide-free controls. Phase determination was carried out using the swelling series (X-ray) and isomorphous derivative (neutron) methods. The water distribution between adjacent bilayers in the stacks may be described by a pair of Gaussians whose position and width change with the protonation state of the melittin. Difference Fourier profiles reveal that the melittin largely incorporates into the phospholipid bilayers. Changes in the water, melittin and deuterium label distributions fit a model in which the melittin lies both at the surface and close to the centre of the bilayer, the distribution of peptide between these locations being pH-dependent, with a larger population of surface melittin when the N-terminus is unprotonated.

Amyloid formation by salmon calcitonin.

It is demonstrated using three independent methods that salmon calcitonin can form amyloid fibrils in vitro. Large aggregates are shown to exhibit a blue-green birefringence in cross polarised light after staining with congo red. Individual fibrils were observed using electron microscopy. These fibrils are approx. 50-60 A in diameter and up to 20,000 A in length and are similar in appearance to those observed in Alzheimer's disease. Finally, X-ray diffraction studies of the large aggregates reveal the cross-beta conformation characteristics of the monomers in the fibre.

The location of amantadine hydrochloride and free base within phospholipid multilayers: a neutron and X-ray diffraction study.

Concomitant neutron and X-ray studies were undertaken in order to locate accurately the anti-influenza and Parkinson's disease drug amantadine in multilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine. The X-ray data were phased using the swelling series method and the neutron data were phased using D2O/H2O exchange and a variation of the isomorphous replacement technique. The sets of data complement each other and reveal two populations of amantadine within the bilayer. One site is close to the bilayer surface, the other is much deeper. The majority of the amantadine occupies the surface site. The relative occupancy, but not the position, of the two locations appears to be dependent upon the initial protonation state of the drug. No evidence of bilayer perturbation was observed with either the protonated or the deprotonated forms of amantadine.